December 18, 2013

A Neandertal from the Altai Mountains (Prüfer et al. 2013)

There seems to have been a lot of inter-"species" sex during the Paleolithic (left), and that's just from a handful of Eurasian hominins sequenced so far.

Who knows what other Middle Paleolithic genomes might be in the works? My guess is that once all is said and done, the tree of Homo will fill up with "red" admixture edges, and those who argued for a single Homo lineage evolving over hundreds of thousands of years, with gene flow between regional populations, will have the upper hand.

An interesting finding is that the introgressing Neandertal (N.I.) was related to the Mezmaiskaya sample from the Caucasus rather than to the Vindija sample from Croatia or the new Altai Neandertal. It'd be great to have the genome of a bona fide "progressive"Near Eastern Neandertal.

UPDATE I (Dec. 19):
Reading the 249 pages of supplementary information is likely to reveal a lot of gems of new information.In SI 13 we see that:

We detect likely West Eurasian gene flow into the ancestors of Yoruba West Africans within the last ten thousand years, which indirectly contributed a small amount of Neandertal ancestry to Yoruba.

and:

These results mean that we have not identified any sub-Saharan African sample that we are confident has no evidence of back-to-Africa migration. Our best candidate at present is the Dinka but it is possible that with a phased genome or large sample sizes we would detect evidence of non-African ancestry in this population as well.

Nature (2013) doi:10.1038/nature12886

The complete genome sequence of a Neanderthal from the Altai Mountains

Kay Prüfer et al.

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

"My guess is that once all is said and done, the tree of Homo will fill up with 'red' admixture edges, and those who argued for a single Homo lineage evolving over hundreds of thousands of years, with gene flow between regional populations, will have the upper hand".

To me the latest findings are making more and more sense. I have never been very convinced by the idea of a single OoA event giving rise to the whole of modern humanity. The 'regional continuity' theory has made complete sense ever since I attended an Alan Thorne lecture in 2001. A sinle origin would lead to such an unacceptable level of inbreeding that humans would not have survived as long as they have.

"You may have read of the tragic case of a highly inbred group of people that has been discovered in Australia, descended from two great grandparents".

I haven't actually. Can you provide details?

"How common would groups like this have been in paleolithic Eurasia?"

Very common would be my guess, as shown by:

"We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors".

In fact new gene mutations and combinations can really only become fixed through inbreeding. They survive when they move into a wider population with the arrival of a new group to interbreed with.

It doesn't seem like a single line at all, just plain old multiregionalism. Your mtdna and y-dna are not your whole ancestry and they will quickly drift out in small groups or if there's selection pressure.

Saying x percent of your genes are neanderthal derived means your neanderthal percentage of parentage is much higher than x because mostly they overlap there's not so many unique ones.

If African groups all have gene back-flow from non African groups, as this paper hints, could the increased genetic diversity of African groups be partly explained by a (until recently) more one-way back-flow of genes? IOW from the time of isolation the Africans keep all of their novel mutations among themselves, but the OOA bunch re-introduce their novel mutations back into Africa, so it looks like Africa has all of theirs plus their own group. If this effect is strong enough, might it strongly influence the gap between the first humans and the OOA bunch?

"we find that the Neanderthal-derived DNA in all non-Africans is more closely related to the Mezmaiskaya Neanderthal from the Caucasus than it is to either the Neanderthal from Siberia ... or to the Vindija Neanderthals from Croatia..."

That makes sense - the Caucasus is closer to N or NE Arabia, where one would suspect admixture to have taken place to failrly uniformly affect all non-African modern humans.

Fig. 4 also makes it plausible that the three groups did not diverge from each other until about 300-400kya, as I postulated in other posts (i.e., heidelbergensis in W Eurasia and Africa had strong bidirectional gene flow, which was disrupted after the onset of the strong cold phase). The last portion of this gene flow appears to have given Neanderthals their female lineage, which is different from the early Spanish speciman and Denisovans.

Using the faster mutation rate, from the paper the Neanderthal and Denisovan combined split from modern humans was about 280 - 290kya (275 - 380kya, method II), that of Neanderthals to Denisovans 190kya (220 - 240kya, method II) - at least roughly similar to my estimates from fig. 4. Also, this would make Denisovans very lateheidelbergensis.

"We estimate the population split time between the introgressing Neanderthal and the Altai Neanderthal genome to 77,000–114,000 (38-57k) years ago, and the split time between the introgressing Denisovan and the Denisovan genome to 276,000–403,000 (138-202k) years ago"

where I inserted in parenthesis the values for the faster mutation rate. Either way, this appears to be inconsistent with my previous suspision that Neanderthal admixture into humans is really (or partially) W Eurasian heidelbergensis, but is again consistent with Denisovans being part of the heidelbergensis branch - which their mtDNA appears to indicate, as well.

I start by saying I usually read this blog to widen my genetics knowledge about the human dispersal around the world, and so I am not an expert in genetics at all. It’s been a long time since I want to make this question. The admixture among different branches of the tree of Homo is a highly probable event (or quite sure), but it’s hard to me to understand the importance and the impact on the history of the present polulations (homo sapiens). I say this regardless the obvious interest by genetists and their studies.I mean, this admixture (low in percentage) does not turn the lineage of homo sapiens into a new one or, I suppose, no one is claiming that the world in currently inhabited by Neandertals admixed with Sapiens.I remember some papers, saying the same, concerning the admixture between first hominids and great apes, but I never have read something about that human lineages are not really human.This sounds as anyone was saying that present (and future) europeans are africans/asian because of recent and low admixture. Sometimes all this seems to me a kind of “paleo-sociology” to revaluate the extinct cousins or like some weird “out-of-america” theories that over-estimate a probable low impact event.

It seems like Svante Paabo and David Reich are foreshadowing their next big project: In the concluding remarks of this paper...

"The estimated population split time is also compatible with the possibility that this unknown hominin was what is known from the fossil record as Homo erectus...However, further work is necessary to establish if and how this gene flow event occurred."

Maybe next year we will have the complete genome sequence of Homo erectus.

"You can also read that in the last million years there has been a minimum of three Out of Africa events".

Possibly so. To me the haplogroup phylogeny , rather than demonstrating a series of expansions from Africa, suggests the basal modern human mt-DNA's ancestor entered Africa from Eurasia. Where it met up with the indigenous Y-DNA and eventually descendants of the two haplogroups moved back out. The 'Caucasian' element in Africans may go back beyond a mere 100,000 years.

"I remember some papers, saying the same, concerning the admixture between first hominids and great apes, but I never have read something about that human lineages are not really human".

Don't forget that after 'mixing' you have 'selection'. It turns out that the transition from 'Archaic' to 'Modern' was not some sudden change but a gradual change of the sort Darwin originally imagined.

"it looks like Africa has all of theirs plus their own group".

That would be correct. There is no doubt that at the deepest level human origins lie in Africa.

"That makes sense - the Caucasus is closer to N or NE Arabia, where one would suspect admixture to have taken place to failrly uniformly affect all non-African modern humans".

And is exactly where we find Y-DNA G today. And probably IJ. Some mt-DNA must be involved as well, perhaps some form(s) of N.

I doubt that the Dinka will be less Eurasian than inner West Africans like the Yoruba. In several haplogroup studies there were residual traces of M/N/R of around 2-4% in South Sudanese populations. Also, on their paternal side, E1b1b is not uncommon among them (although A and B dominate) and we know that E1b1b is often linked to Red Sea autosomal affinities.

I wrote, 'The 'Caucasian element in Africans may go back beyond a mere 100,000 years'. Unlikely. From the update:

"We detect likely West Eurasian gene flow into the ancestors of Yoruba West Africans within the last ten thousand years, which indirectly contributed a small amount of Neandertal ancestry to Yoruba".

So it is not 'ancient'.

"the link to the story about the Australian family is here"

Thanks for that.

Quote:

"Sadly, a number of those children have come into the world with birth defects — a boy with misaligned eyes, another with a walking impairment, a child with hearing and sight problems, another with stunted speech".

I would guess miscarraiges prevented a proportion of inbred offspring from even being born. The story is careful to avoid saying where the family is but the photograph with the caption, 'The camp lay 20 miles from the nearest town in New South Wales, pictured, near Sydney' is of the Three Sisters at Katoomba, very near where I used to live.

SIMPLIFIED DIAGRAM OF THE PROCESS OF THE DIFFERENTIATION OF THE RACES UNDER THE INFLUENCE OF PHYSICAL FACTORS

- Appearance of the Yellow race, 15,000 years ago at the very earliest, perhaps during the Mesolithic Age, resulting in the interbreeding of Black and White in the cold climate- Appearance of the first Cro-Magnon, 20,000 years ago- (period of differentiation between the Grimaldi and the Cro-Magnon)- Arrival in Europe of the African Homo sapiens sapiens( Grimaldi Negroid), 40,000 years ago- Homo sabiens sapiens ( African), Omo I, Kanjera to approximately 1,000,000 years ago- (Neanderthal Man: Broken Hill, 110,000 years ago. La-Chappelle-aux-Saint, 80,000 year ago)- Homo habilis( African), 2,500,000 years ago.- Australopithecus gracile and robustus, approximately 5,500,000-2,000,000 years ago

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